Thayer was born in Lawrence, Massachusetts and raised in Worcester. He graduated magna cum laude in philosophy from Harvard in 1885, where he was editor of the Harvard Lampoon. Its business manager, William Randolph Hearst, hired Thayer as humor columnist for the San Francisco Examiner 1886-88.

Thayer’s last piece, dated June 3, 1888, was a ballad entitled "Casey" ("Casey at the Bat").

It took several months after its publication for the poem to make Thayer famous, since he was hardly the boastful type and had signed the June 3 poem with the nickname "Phin". Two mysteries remain about the poem: whether anyone or anyplace was the real-life Casey and Mudville, and, if so, their actual identities. On March 31, 2004, Katie Zezima of The New York Times penned an article called "In 'Casey' Rhubarb, 2 Cities Cry 'Foul!'" on the competing claims of two towns to such renown: Stockton, California, and Holliston, Massachusetts.

On the possible model for Casey, Thayer dismissed the notion that any single living baseball player was an influence. However, late 1880s Boston star Mike "King" Kelly is odds-on the most likely model for Casey's baseball situations. Besides being a native of a town close to Boston, Thayer, as a San Francisco Examiner baseball reporter in the offseason of 1887-88, covered exhibition games featuring Kelly. In November 1887, some of his reportage about a Kelly at-bat has the same ring as Casey's famous at-bat in the poem. A 2004 book by Howard W. Rosenberg, Cap Anson 2: The Theatrical and Kingly Mike Kelly: U.S. Team Sport's First Media Sensation and Baseball's Original Casey at the Bat, reprints a 1905 Thayer letter to a Baltimore scribe who was asking about the poem's roots. In the letter, Thayer singled out Kelly (d. 1894), as having shown "impudence" in claiming to have written it. Rosenberg argues that if Thayer still felt offended, Thayer may have steered later comments away from connecting Kelly to it. Kelly had also performed in vaudeville, and recited the poem dozens of times, possibly, to Thayer's dismay, butchering it. Incidentally, the first public performance of the poem was on August 14, 1888, by actor De Wolf Hopper, on Thayer's 25th birthday.

Thayer's recitation of it at a Harvard class reunion in 1895 may seem trivial except that it helps solve the mystery, which lingered into the 20th century, of who had written it. In the mid-1890s, Thayer contributed several other comic poems for Hearst's New York Journal and then turned to overseeing his family's mills in Worcester full-time.

Thayer moved to Santa Barbara in 1912, where he married Rosalind Buel Hammett and retired. He died in 1940, at age 77.

The New York Times' obituary of Thayer on August 22, 1940, p. 19 quotes comedian DeWolf Hopper, who helped make the poem famous:

"Thayer indubitably wrote 'Casey,' but he could not recite it.... I have heard many other give 'Casey.' Fond mamas have brought their sons to me to hear their childish voices lisp the poem, but Thayer's was the worst of all. In a sweet, dulcet Harvard whisper he implored 'Casey' to murder the umpire, and gave this cry of mass animal rage all the emphasis of a caterpillar wearing rubbers crawling on a velvet carpet. He was rotten."